BN1022 Genetic Spatial Mapping Report

Genetic Spatial Mapping Plot

This plot shows the spatial genetic mapping results across different tissues.

Cauchy Combination Result

This table presents the results of the Cauchy combination test, summarizing the genetic associations.

Annotation P Cauchy P Median
Layer 3 3.1380e-05 1.2259e-02
Layer 5 4.7851e-05 1.9228e-03
Layer 4 8.7452e-05 4.8732e-03
Layer 2 2.5631e-04 2.0874e-02
Layer 6 6.7345e-04 7.5441e-03
WM 1.8806e-03 8.8325e-02

Diagnosis Manhattan Plot

The Manhattan plot shows the association of SNPs with the top associated gene across the genome.

Gene Expression and GSS Distribution

Select a gene to view its expression distribution and gene specificity score (GSS).

Expression Distribution
KIF1A Expression Distribution
Gene Specificity Score (GSS)
KIF1A GSS Distribution

Top 50 Gene Diagnostic Info

This table lists the top 50 genes based on diagnostic criteria, including the gene specificity score (GSS) and PCC.

Gene Annotation Median GSS PCC
KIF1A Layer 5 2.4883 0.6522
SLC22A17 Layer 3 2.6074 0.6453
ALDOC Layer 3 2.4941 0.6395
APBB1 Layer 5 2.3398 0.6375
RTN3 Layer 5 2.5117 0.6352
UBC Layer 3 2.2646 0.6348
ATP5F1B Layer 3 2.5664 0.6280
AP2M1 Layer 5 2.6602 0.6229
ACTG1 Layer 5 2.1895 0.6224
SNCA Layer 5 2.2549 0.6192
MORF4L1 Layer 5 2.7363 0.6164
NDRG4 Layer 5 2.9805 0.6112
ITPK1 Layer 5 2.3027 0.6099
GDI1 Layer 5 2.3926 0.6082
CKB Layer 3 2.2227 0.6081
NDUFB8 Layer 5 2.2930 0.6067
HSP90AB1 Layer 5 2.2227 0.6051
PLD3 Layer 5 2.6602 0.6038
TLE5 Layer 5 2.5195 0.6024
PSAP Layer 5 2.2715 0.6023
SNRPN Layer 5 2.6777 0.6019
SPTBN1 Layer 5 2.4336 0.6016
CFL1 Layer 6 2.1250 0.6008
FKBP8 Layer 5 2.2168 0.5999
PRKAR1B Layer 5 3.0391 0.5994
CALM2 Layer 3 2.2520 0.5994
YWHAG Layer 5 2.6309 0.5982
CALM1 Layer 2 2.2773 0.5979
SEZ6L2 Layer 5 2.6836 0.5977
PGK1 Layer 5 2.1650 0.5974
CLSTN1 Layer 5 2.6602 0.5973
ENO2 Layer 5 2.7910 0.5968
ATP1B1 Layer 5 2.2129 0.5951
GPI Layer 5 2.4668 0.5943
RTN4 Layer 5 2.3369 0.5938
VAMP2 Layer 5 2.5000 0.5936
CLIP3 Layer 5 2.6074 0.5936
GLUL Layer 3 2.3809 0.5931
PRNP Layer 2 2.6777 0.5928
COX4I1 Layer 3 2.2324 0.5918
TUBA1B Layer 5 2.3750 0.5918
ARPP19 Layer 2 2.6953 0.5915
GNAS Layer 3 2.3594 0.5914
ATP6V0C Layer 3 2.3496 0.5914
TMSB10 Layer 5 2.2969 0.5907
GPX4 Layer 3 2.3965 0.5899
RTN1 Layer 5 2.5898 0.5896
GNB1 Layer 5 2.3594 0.5894
UCHL1 Layer 5 2.7158 0.5892
B4GAT1 Layer 5 2.2266 0.5890

Running Info

Click to view detailed run information and parameters.

gsMap Version: 1.73.0

Parameters:

  • Sample Name: BN1022
  • Trait Name: PD
  • Summary Statistics File: /mnt/data/projects/ASAP/ST/gsMAP/GWAS_nallsEtAl2019_allSamples_allVariants.sumstats.gz
  • HDF5 Path: /mnt/data/projects/ASAP/ST/gsMAP/st_anndata_h5ads/st_adata_BN1022_for_gsmap.h5ad
  • Annotation: smoothed_label_s5
  • Spatial LDSC Save Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1022/spatial_ldsc
  • Cauchy Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1022/cauchy_combination
  • Report Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1022/report/PD
  • gsMap Report File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1022/report/PD/BN1022_PD_gsMap_Report.html
  • Gene Diagnostic Info File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1022/report/PD/BN1022_PD_Gene_Diagnostic_Info.csv
  • Report Generation Date: 2025-04-11 02:07:31
  • Number of Processes: 10
  • Spending Time: 0h 4m